Mercurial > repos > lecorguille > msnbase_readmsdata
diff lib.r @ 10:84533814b1d5 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
| author | lecorguille |
|---|---|
| date | Mon, 29 Apr 2019 06:07:14 -0400 |
| parents | 3d8a68b45153 |
| children | cda005bc221c |
line wrap: on
line diff
--- a/lib.r Fri Feb 08 09:55:50 2019 -0500 +++ b/lib.r Mon Apr 29 06:07:14 2019 -0400 @@ -69,7 +69,7 @@ chromBPI_adjusted_merged <- chromBPI_adjusted } else { if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata) - else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata) + else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged,xdata) else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata") singlefile_merged <- c(singlefile_merged,singlefile) @@ -333,7 +333,7 @@ files[exists] <- sub("//","/",files[exists]) # WHAT IS ON THE FILESYSTEM - filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T) + filesystem_filepaths <- system(paste0("find \"",getwd(),"/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T) filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)] # COMPARISON